tag:blogger.com,1999:blog-36768584.post5085885893689974891..comments2018-03-16T11:24:44.723-04:00Comments on Omics! Omics!: Oxford Takes Some Flak, Fires BackKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-36768584.post-69331902474829074732014-09-08T09:54:58.079-04:002014-09-08T09:54:58.079-04:00Thanks Keith for an informative post. I was surpri...Thanks Keith for an informative post. I was surprised to see such a negative paper (as you mention, &#39;constructive criticism&#39; is absent) published.<br /><br />Nice to see that there have been many rapid iterations for a platform that is widely watched, and certainly one group&#39;s early experience going &#39;on the record&#39; it can be easily discounted with additional publications with more recent chemistry.<br /><br />Interesting effect on the library prep&#39;s effect on the sequencing. Any thoughts on why this is the case? (I.e. is that same pronounced effect seen on PacBio data, or is this something unique to the nanopore method?)Dale Yuzukihttps://www.blogger.com/profile/06793338970769363594noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-20328448147040283122014-09-07T09:54:08.187-04:002014-09-07T09:54:08.187-04:00&quot;http://flxlexblog.wordpress.com/2014/02/14/t...&quot;http://flxlexblog.wordpress.com/2014/02/14/the-one-and-only-oxford-nanopore-talk-at-agbt-2014-with-real-data/&quot;<br /><br />they have a small and ongoing collaboration with David Jaffe - not an early access agreement with Broad.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-48400999867781151582014-09-07T09:53:09.575-04:002014-09-07T09:53:09.575-04:00&quot;Did not ONT already go through that show?&qu...&quot;Did not ONT already go through that show?&quot;<br /><br />no they didnt MAP was their first shipping.<br /><br />This whole thing looks pre-meditated and malicious.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-90117381526024133962014-09-07T08:35:28.014-04:002014-09-07T08:35:28.014-04:00One bad review won&#39;t kill an early access prog...One bad review won&#39;t kill an early access program. A decision to bring in ONT as a possible sequencing technology requires a risk assessment about a nano-tech system: that requires a broad understanding of both the state of the technology, the financial backing provided by ONT, the pain points that sequencing technologies exhibit, and the opportunities that the market provides. One bad review is irrelevant in this evaluation, so I am not worried about its impact. The problem ONT is trying to solve is deep, but its impact would be massive, transformative, and ever lasting. Let&#39;s hope the financial backers are in it for the long haul. Theodore Omtzigthttps://www.blogger.com/profile/18249997607495408266noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-27740706760081015212014-09-07T02:24:58.545-04:002014-09-07T02:24:58.545-04:00&quot;Prior advance access programs for genomic te...&quot;Prior advance access programs for genomic technologies have generally involved a select set of elite genome centers and ironclad legal contracts controlling data release and comment.&quot;<br /><br />Did not ONT already go through that show?<br /><br />http://flxlexblog.wordpress.com/2014/02/14/the-one-and-only-oxford-nanopore-talk-at-agbt-2014-with-real-data/Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-64856957810292984562014-09-06T16:29:02.738-04:002014-09-06T16:29:02.738-04:00I like the abstract comment &quot;at best 890±1,93...I like the abstract comment &quot;at best 890±1,932 bases per mapped read&quot;. It highlights the rushed nature of the report. Surely &quot;at best&quot; is the upper bound 890+1932=2822? Still, imagine every base in every read mapped. Then their computation averages and computes a variance across reads. So the statement wouldn&#39;t represent the variability in the mapping just the variability in the input DNA length. Surely a proportion mapping would better suit? Or would it? If the reads contain large sections that don&#39;t map, for whatever reason, then the proportion would again average over non homogenous mappings. What should be reported then? Chunk the data into 500mers and report the mode together with measure of spread?Anonymousnoreply@blogger.com